1
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Molodtseva AS, Makunin AI, Salomashkina VV, Kichigin IG, Vorobieva NV, Vasiliev SK, Shunkov MV, Tishkin AA, Grushin SP, Anijalg P, Tammeleht E, Keis M, Boeskorov GG, Mamaev N, Okhlopkov IM, Kryukov AP, Lyapunova EA, Kholodova MV, Seryodkin IV, Saarma U, Trifonov VA, Graphodatsky AS. Phylogeography of ancient and modern brown bears from eastern Eurasia. Biol J Linn Soc Lond 2022; 135:722-733. [PMID: 35359699 PMCID: PMC8943912 DOI: 10.1093/biolinnean/blac009] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 11/12/2022]
Abstract
The brown bear (Ursus arctos) is an iconic carnivoran species of the Northern Hemisphere. Its population history has been studied extensively using mitochondrial markers, which demonstrated signatures of multiple waves of migration, arguably connected with glaciation periods. Among Eurasian brown bears, Siberian populations remain understudied. We have sequenced complete mitochondrial genomes of four ancient (~4.5-40 kya) bears from South Siberia and 19 modern bears from South Siberia and the Russian Far East. Reconstruction of phylogenetic relationships between haplotypes and evaluation of modern population structure have demonstrated that all the studied samples belong to the most widespread Eurasian clade 3. One of the ancient haplotypes takes a basal position relative to the whole of clade 3; the second is basal to the haplogroup 3a (the most common subclade), and two others belong to clades 3a1 and 3b. Modern Siberian bears retain at least some of this diversity; apart from the most common haplogroup 3a, we demonstrate the presence of clade 3b, which was previously found mainly in mainland Eurasia and Northern Japan. Our findings highlight the importance of South Siberia as a refugium for northern Eurasian brown bears and further corroborate the hypothesis of several waves of migration in the Pleistocene.
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Affiliation(s)
- Anna S Molodtseva
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexey I Makunin
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia,Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | | | - Ilya G Kichigin
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Nadezhda V Vorobieva
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Sergey K Vasiliev
- Institute of Archaeology and Ethnography, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Mikhail V Shunkov
- Institute of Archaeology and Ethnography, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | | | | | - Peeter Anijalg
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Egle Tammeleht
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Marju Keis
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Gennady G Boeskorov
- Geological Museum, Institute of Diamond and Precious Metals Geology, Siberian Branch of the Russian Academy of Sciences, Yakutsk, Russia
| | - Nikolai Mamaev
- Institute for Biological Problems of Cryolithozone, Siberian Branch of the Russian Academy of Sciences, Yakutsk, Russia
| | - Innokenty M Okhlopkov
- Institute for Biological Problems of Cryolithozone, Siberian Branch of the Russian Academy of Sciences, Yakutsk, Russia
| | - Alexey P Kryukov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Elena A Lyapunova
- N. K. Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
| | - Marina V Kholodova
- A. N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Ivan V Seryodkin
- Pacific Institute of Geography, Far East Branch, Russian Academy of Sciences, Vladivostok, Russia
| | - Urmas Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | | | - Alexander S Graphodatsky
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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2
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Buggiotti L, Yurchenko AA, Yudin NS, Vander Jagt CJ, Vorobieva NV, Kusliy MA, Vasiliev SK, Rodionov AN, Boronetskaya OI, Zinovieva NA, Graphodatsky AS, Daetwyler HD, Larkin DM. Demographic History, Adaptation, and NRAP Convergent Evolution at Amino Acid Residue 100 in the World Northernmost Cattle from Siberia. Mol Biol Evol 2021; 38:3093-3110. [PMID: 33784744 PMCID: PMC8321547 DOI: 10.1093/molbev/msab078] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Native cattle breeds represent an important cultural heritage. They are a reservoir of genetic variation useful for properly responding to agriculture needs in the light of ongoing climate changes. Evolutionary processes that occur in response to extreme environmental conditions could also be better understood using adapted local populations. Herein, different evolutionary histories of the world northernmost native cattle breeds from Russia were investigated. They highlighted Kholmogory as a typical taurine cattle, whereas Yakut cattle separated from European taurines approximately 5,000 years ago and contain numerous ancestral and some novel genetic variants allowing their adaptation to harsh conditions of living above the Polar Circle. Scans for selection signatures pointed to several common gene pathways related to adaptation to harsh climates in both breeds. But genes affected by selection from these pathways were mostly different. A Yakut cattle breed-specific missense mutation in a highly conserved NRAP gene represents a unique example of a young amino acid residue convergent change shared with at least 16 species of hibernating/cold-adapted mammals from six distinct phylogenetic orders. This suggests a convergent evolution event along the mammalian phylogenetic tree and fast fixation in a single isolated cattle population exposed to a harsh climate.
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Affiliation(s)
- Laura Buggiotti
- Royal Veterinary College, University of London, London, United Kingdom
| | - Andrey A Yurchenko
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
- Kurchatov Genomics Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Science, Novosibirsk, Russia
| | - Nikolay S Yudin
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
- Kurchatov Genomics Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Science, Novosibirsk, Russia
| | | | - Nadezhda V Vorobieva
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Mariya A Kusliy
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Sergei K Vasiliev
- Paleometal Archeology Department, Institute of Archaeology and Ethnography SB RAS, Novosibirsk, Russia
| | - Andrey N Rodionov
- L.K. Ernst Federal Research Centre for Animal Husbandry, Podolsk, Russia
| | - Oksana I Boronetskaya
- Moscow Agrarian Academy, Timiryazev Russian State Agrarian University, Moscow, Russia
| | | | - Alexander S Graphodatsky
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Hans D Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Denis M Larkin
- Royal Veterinary College, University of London, London, United Kingdom
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
- Kurchatov Genomics Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Science, Novosibirsk, Russia
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3
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Dog domestication and the dual dispersal of people and dogs into the Americas. Proc Natl Acad Sci U S A 2021; 118:2010083118. [PMID: 33495362 DOI: 10.1073/pnas.2010083118] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Advances in the isolation and sequencing of ancient DNA have begun to reveal the population histories of both people and dogs. Over the last 10,000 y, the genetic signatures of ancient dog remains have been linked with known human dispersals in regions such as the Arctic and the remote Pacific. It is suspected, however, that this relationship has a much deeper antiquity, and that the tandem movement of people and dogs may have begun soon after the domestication of the dog from a gray wolf ancestor in the late Pleistocene. Here, by comparing population genetic results of humans and dogs from Siberia, Beringia, and North America, we show that there is a close correlation in the movement and divergences of their respective lineages. This evidence places constraints on when and where dog domestication took place. Most significantly, it suggests that dogs were domesticated in Siberia by ∼23,000 y ago, possibly while both people and wolves were isolated during the harsh climate of the Last Glacial Maximum. Dogs then accompanied the first people into the Americas and traveled with them as humans rapidly dispersed into the continent beginning ∼15,000 y ago.
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4
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Burrows AM, Kaminski J, Waller BM, Omstead KM, Rogers-Vizena C, Mendelson B. Dog faces exhibit anatomical differences in comparison to other domestic animals. Anat Rec (Hoboken) 2020; 304:231-241. [PMID: 32969196 DOI: 10.1002/ar.24507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/24/2020] [Accepted: 06/27/2020] [Indexed: 11/11/2022]
Affiliation(s)
- Anne M Burrows
- Department of Physical Therapy, Duquesne University, Pittsburgh, Pennsylvania, USA.,Department of Anthropology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Juliane Kaminski
- Department of Psychology, University of Portsmouth, Portsmouth, UK
| | - Bridget M Waller
- Department of Psychology, University of Portsmouth, Portsmouth, UK
| | - Kailey M Omstead
- Department of Physical Therapy, Duquesne University, Pittsburgh, Pennsylvania, USA
| | - Carolyn Rogers-Vizena
- Department of Plastic & Oral Surgery, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Bryan Mendelson
- The Centre for Facial Plastic Surgery, Melbourne, Victoria, Australia
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5
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Nikolsky A. The Pastoral Origin of Semiotically Functional Tonal Organization of Music. Front Psychol 2020; 11:1358. [PMID: 32848961 PMCID: PMC7396614 DOI: 10.3389/fpsyg.2020.01358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 05/22/2020] [Indexed: 11/13/2022] Open
Abstract
This paper presents a new line of inquiry into when and how music as a semiotic system was born. Eleven principal expressive aspects of music each contains specific structural patterns whose configuration signifies a certain affective state. This distinguishes the tonal organization of music from the phonetic and prosodic organization of natural languages and animal communication. The question of music’s origin can therefore be answered by establishing the point in human history at which all eleven expressive aspects might have been abstracted from the instinct-driven primate calls and used to express human psycho-emotional states. Etic analysis of acoustic parameters is the prime means of cross-examination of the typical patterns of expression of the basic emotions in human music versus animal vocal communication. A new method of such analysis is proposed here. Formation of such expressive aspects as meter, tempo, melodic intervals, and articulation can be explained by the influence of bipedal locomotion, breathing cycle, and heartbeat, long before Homo sapiens. However, two aspects, rhythm and melodic contour, most crucial for music as we know it, lack proxies in the Paleolithic lifestyle. The available ethnographic and developmental data leads one to believe that rhythmic and directional patterns of melody became involved in conveying emotion-related information in the process of frequent switching from one call-type to another within the limited repertory of calls. Such calls are usually adopted for the ongoing caretaking of human youngsters and domestic animals. The efficacy of rhythm and pitch contour in affective communication must have been spontaneously discovered in new important cultural activities. The most likely scenario for music to have become fully semiotically functional and to have spread wide enough to avoid extinctions is the formation of cross-specific communication between humans and domesticated animals during the Neolithic demographic explosion and the subsequent cultural revolution. Changes in distance during such communication must have promoted the integration between different expressive aspects and generated the basic musical grammar. The model of such communication can be found in the surviving tradition of Scandinavian pastoral music - kulning. This article discusses the most likely ways in which such music evolved.
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6
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Loog L, Thalmann O, Sinding MHS, Schuenemann VJ, Perri A, Germonpré M, Bocherens H, Witt KE, Samaniego Castruita JA, Velasco MS, Lundstrøm IKC, Wales N, Sonet G, Frantz L, Schroeder H, Budd J, Jimenez EL, Fedorov S, Gasparyan B, Kandel AW, Lázničková-Galetová M, Napierala H, Uerpmann HP, Nikolskiy PA, Pavlova EY, Pitulko VV, Herzig KH, Malhi RS, Willerslev E, Hansen AJ, Dobney K, Gilbert MTP, Krause J, Larson G, Eriksson A, Manica A. Ancient DNA suggests modern wolves trace their origin to a Late Pleistocene expansion from Beringia. Mol Ecol 2020; 29:1596-1610. [PMID: 31840921 PMCID: PMC7317801 DOI: 10.1111/mec.15329] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 10/16/2019] [Accepted: 12/03/2019] [Indexed: 01/21/2023]
Abstract
Grey wolves (Canis lupus) are one of the few large terrestrial carnivores that have maintained a wide geographical distribution across the Northern Hemisphere throughout the Pleistocene and Holocene. Recent genetic studies have suggested that, despite this continuous presence, major demographic changes occurred in wolf populations between the Late Pleistocene and early Holocene, and that extant wolves trace their ancestry to a single Late Pleistocene population. Both the geographical origin of this ancestral population and how it became widespread remain unknown. Here, we used a spatially and temporally explicit modelling framework to analyse a data set of 90 modern and 45 ancient mitochondrial wolf genomes from across the Northern Hemisphere, spanning the last 50,000 years. Our results suggest that contemporary wolf populations trace their ancestry to an expansion from Beringia at the end of the Last Glacial Maximum, and that this process was most likely driven by Late Pleistocene ecological fluctuations that occurred across the Northern Hemisphere. This study provides direct ancient genetic evidence that long‐range migration has played an important role in the population history of a large carnivore, and provides insight into how wolves survived the wave of megafaunal extinctions at the end of the last glaciation. Moreover, because Late Pleistocene grey wolves were the likely source from which all modern dogs trace their origins, the demographic history described in this study has fundamental implications for understanding the geographical origin of the dog. see also the Perspective by Rena M. Schweizer and Robert K. Wayne.
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Affiliation(s)
- Liisa Loog
- Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.,Department of Zoology, University of Cambridge, Cambridge, UK.,Manchester Institute of Biotechnology, School of Earth and Environmental Sciences, University of Manchester, Manchester, UK.,Department of Genetics, University of Cambridge, Cambridge, UK
| | - Olaf Thalmann
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Mikkel-Holger S Sinding
- EvoGenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Natural History Museum, University of Oslo, Oslo, Norway.,The Qimmeq Project, University of Greenland, Nuussuaq, Greenland
| | - Verena J Schuenemann
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.,Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany.,Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Angela Perri
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mietje Germonpré
- OD Earth and History of Life, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Herve Bocherens
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany.,Department of Geosciences, Palaeobiology, University of Tübingen, Tübingen, Germany
| | - Kelsey E Witt
- School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Marcela S Velasco
- EvoGenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Inge K C Lundstrøm
- EvoGenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Nathan Wales
- EvoGenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,BioArch, Department of Archaeology, University of York, York, UK, USA
| | - Gontran Sonet
- OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Laurent Frantz
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Hannes Schroeder
- EvoGenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jane Budd
- Breeding Centre for Endangered Arabian Wildlife, Sharjah, United Arab Emirates
| | - Elodie-Laure Jimenez
- OD Earth and History of Life, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Sergey Fedorov
- Mammoth Museum, Institute of Applied Ecology of the North of the North-Eastern Federal University, Yakutsk, Russia
| | - Boris Gasparyan
- Institute of Archaeology and Ethnography, National Academy of Sciences of the Republic of Armenia, Yerevan, Republic of Armenia
| | - Andrew W Kandel
- Heidelberg Academy of Sciences and Humanities: The Role of Culture in Early Expansions of Humans, Tübingen, Germany
| | - Martina Lázničková-Galetová
- Department of Anthropology, University of West Bohemia, Pilzen, Czech Republic.,Moravian museum, Brno, Czech Republic.,Hrdlička Museum of Man, Faculty of Science, Charles University, Praha, Czech Republic
| | - Hannes Napierala
- Institute of Palaeoanatomy, Domestication Research and History of Veterinary Medicine, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Hans-Peter Uerpmann
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Pavel A Nikolskiy
- Geological Institute, Russian Academy of Sciences, Moscow, Russia.,Institute for Material Culture History, Russian Academy of Sciences, St Petersburg, Russia
| | - Elena Y Pavlova
- Institute for Material Culture History, Russian Academy of Sciences, St Petersburg, Russia.,Arctic and Antarctic Research Institute, St Petersburg, Russia
| | - Vladimir V Pitulko
- Institute for Material Culture History, Russian Academy of Sciences, St Petersburg, Russia
| | - Karl-Heinz Herzig
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland.,Institute of Biomedicine and Biocenter of Oulu, Medical Research Center and University Hospital, University of Oulu, Oulu, Finland
| | - Ripan S Malhi
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Eske Willerslev
- Department of Zoology, University of Cambridge, Cambridge, UK.,Centre for GeoGenetics Globe Institute, University of Copenhagen, Copenhagen, Denmark.,Wellcome Trust Sanger Institute, Cambridge, UK
| | - Anders J Hansen
- The Qimmeq Project, University of Greenland, Nuussuaq, Greenland.,Centre for GeoGenetics Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Keith Dobney
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK.,Department of Archaeology, University of Aberdeen, Aberdeen, UK.,Department of Archaeology, Simon Fraser University, Burnaby, BC, Canada
| | - M Thomas P Gilbert
- EvoGenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Norwegian University of Science and Technology, University Museum, Trondheim, Norway
| | - Johannes Krause
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.,Max Planck Institute for the Science of Human History, Jena, Germany
| | - Greger Larson
- Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Anders Eriksson
- Department of Zoology, University of Cambridge, Cambridge, UK.,Department of Medical & Molecular Genetics, King's College London, Guys Hospital, London, UK.,cGEM, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Cambridge, UK
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7
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The relations between evolution and domestication reconsidered - Implications for systematics, ecology, and nature conservation. Glob Ecol Conserv 2019. [DOI: 10.1016/j.gecco.2019.e00756] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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8
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Antonova EI, Solovyev AV, Vyazov LA, Semykin YA, Mishchenko AV. Reconstruction of the Mitochondrial Genome of the Ancient Horse from the Ashna-Pando Hillfort (Middle Volga). RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419050041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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9
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Varga B, Gergely A, Galambos Á, Kis A. Heart Rate and Heart Rate Variability during Sleep in Family Dogs ( Canis familiaris). Moderate Effect of Pre-Sleep Emotions. Animals (Basel) 2018; 8:ani8070107. [PMID: 30004461 PMCID: PMC6071078 DOI: 10.3390/ani8070107] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 06/06/2018] [Accepted: 06/23/2018] [Indexed: 12/11/2022] Open
Abstract
Simple Summary It is common knowledge that negative emotions in humans are accompanied by both impaired subjective experience as well as maladaptive changes in behavior and physiology. The present paper investigates heart rate—one of the most commonly used emotion-related physiology measures—in the family dog, with the aim of uncovering its potential relationship with emotions. Sleep recordings were conducted following a positive versus a negative social interaction, as sleep alternations are one of the most conspicuous changes in response to negative affect. We observed differences in heart rate following the positive versus negative interactions, however these were only apparent during wakefulness, but not during sleep. Abstract The domestic dog (Canis familiaris) has been shown to both excel in recognising human emotions and produce emotion-related vocalisations and postures that humans can easily recognise. However, little is known about the effect of emotional experiences on subsequent sleep physiology, a set of phenomena heavily interrelated with emotions in the case of humans. The present paper examines heart rate (HR) and heart rate variability (HRV) during dogs’ sleep, measures that are influenced by both positive and negative emotions in awake dogs. In Study I, descriptive HR and HRV data is provided on N = 12 dogs about the different sleep stages (wake, drowsiness, non-rapid eye movement (non-REM), REM; scoring based on electroencephalogram (EEG) data). We conclude that wakefulness is characterised by higher HR and lower HRV compared to all sleep stages. Furthermore, drowsiness is characterised by higher HR and lower HRV than non-REM and REM, but only if the electrocardiogram (ECG) samples are taken from the first occurrence of a given sleep stage, not when the longest periods of each sleep stage are analysed. Non-REM and REM sleep were not found to be different from each other in either HR or HRV parameters. In Study II, sleep HR and HRV measures are compared in N = 16 dogs after a positive versus negative social interaction (within-subject design). The positive social interaction consisted of petting and ball play, while the negative social interaction was a mixture of separation, threatening approach and still face test. Results are consistent with the two-dimensional emotion hypothesis in that following the intense positive interaction more elevated HR and decreased HRV is found compared to the mildly negative (lower intensity) interaction. However, although this trend can be observed in all sleep stages except for REM, the results only reach significance in the wake stage. In sum, the present findings suggest that HR and HRV are possible to measure during dogs’ sleep, and can potentially be used to study the effect of emotions not only during but also after such interactions.
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Affiliation(s)
- Bence Varga
- Institute of Cognitive Neuroscience and Psychology, Hungarian Academy of Sciences, 1117 Budapest, Hungary.
- Department of Cognitive Science, Budapest University of Technology and Economics, 1111 Budapest, Hungary.
| | - Anna Gergely
- Institute of Cognitive Neuroscience and Psychology, Hungarian Academy of Sciences, 1117 Budapest, Hungary.
| | - Ágoston Galambos
- Institute of Cognitive Neuroscience and Psychology, Hungarian Academy of Sciences, 1117 Budapest, Hungary.
- Department of Cognitive Psychology, Eötvös Loránd University, 1053 Budapest, Hungary.
| | - Anna Kis
- Institute of Cognitive Neuroscience and Psychology, Hungarian Academy of Sciences, 1117 Budapest, Hungary.
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10
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Cairns KM, Shannon LM, Koler-Matznick J, Ballard JWO, Boyko AR. Elucidating biogeographical patterns in Australian native canids using genome wide SNPs. PLoS One 2018; 13:e0198754. [PMID: 29889854 PMCID: PMC5995383 DOI: 10.1371/journal.pone.0198754] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 05/24/2018] [Indexed: 11/19/2022] Open
Abstract
Dingoes play a strong role in Australia's ecological framework as the apex predator but are under threat from hybridization and agricultural control programs. Government legislation lists the conservation of the dingo as an important aim, yet little is known about the biogeography of this enigmatic canine, making conservation difficult. Mitochondrial and Y chromosome DNA studies show evidence of population structure within the dingo. Here, we present the data from Illumina HD canine chip genotyping for 23 dingoes from five regional populations, and five New Guinea Singing Dogs to further explore patterns of biogeography using genome-wide data. Whole genome single nucleotide polymorphism (SNP) data supported the presence of three distinct dingo populations (or ESUs) subject to geographical subdivision: southeastern (SE), Fraser Island (FI) and northwestern (NW). These ESUs should be managed discretely. The FI dingoes are a known reservoir of pure, genetically distinct dingoes. Elevated inbreeding coefficients identified here suggest this population may be genetically compromised and in need of rescue; current lethal management strategies that do not consider genetic information should be suspended until further data can be gathered. D statistics identify evidence of historical admixture or ancestry sharing between southeastern dingoes and South East Asian village dogs. Conservation efforts on mainland Australia should focus on the SE dingo population that is under pressure from domestic dog hybridization and high levels of lethal control. Further data concerning the genetic health, demographics and prevalence of hybridization in the SE and FI dingo populations is urgently needed to develop evidence based conservation and management strategies.
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Affiliation(s)
- Kylie M. Cairns
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
- * E-mail: ,
| | - Laura M. Shannon
- Department of Biomedical Sciences, Cornell University, Ithaca, New York, United States of America
| | - Janice Koler-Matznick
- The New Guinea Singing Dog Conservation Society, Central Point, Oregon, United States of America
| | - J. William O. Ballard
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Adam R. Boyko
- Department of Biomedical Sciences, Cornell University, Ithaca, New York, United States of America
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11
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Parker HG, Dreger DL, Rimbault M, Davis BW, Mullen AB, Carpintero-Ramirez G, Ostrander EA. Genomic Analyses Reveal the Influence of Geographic Origin, Migration, and Hybridization on Modern Dog Breed Development. Cell Rep 2018; 19:697-708. [PMID: 28445722 DOI: 10.1016/j.celrep.2017.03.079] [Citation(s) in RCA: 209] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/10/2017] [Accepted: 03/28/2017] [Indexed: 11/30/2022] Open
Abstract
There are nearly 400 modern domestic dog breeds with a unique histories and genetic profiles. To track the genetic signatures of breed development, we have assembled the most diverse dataset of dog breeds, reflecting their extensive phenotypic variation and heritage. Combining genetic distance, migration, and genome-wide haplotype sharing analyses, we uncover geographic patterns of development and independent origins of common traits. Our analyses reveal the hybrid history of breeds and elucidate the effects of immigration, revealing for the first time a suggestion of New World dog within some modern breeds. Finally, we used cladistics and haplotype sharing to show that some common traits have arisen more than once in the history of the dog. These analyses characterize the complexities of breed development, resolving longstanding questions regarding individual breed origination, the effect of migration on geographically distinct breeds, and, by inference, transfer of trait and disease alleles among dog breeds.
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Affiliation(s)
- Heidi G Parker
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dayna L Dreger
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Maud Rimbault
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Brian W Davis
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexandra B Mullen
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gretchen Carpintero-Ramirez
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Elaine A Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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12
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Marciniak S, Perry GH. Harnessing ancient genomes to study the history of human adaptation. Nat Rev Genet 2017; 18:659-674. [PMID: 28890534 DOI: 10.1038/nrg.2017.65] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The past several years have witnessed an explosion of successful ancient human genome-sequencing projects, with genomic-scale ancient DNA data sets now available for more than 1,100 ancient human and archaic hominin (for example, Neandertal) individuals. Recent 'evolution in action' analyses have started using these data sets to identify and track the spatiotemporal trajectories of genetic variants associated with human adaptations to novel and changing environments, agricultural lifestyles, and introduced or co-evolving pathogens. Together with evidence of adaptive introgression of genetic variants from archaic hominins to humans and emerging ancient genome data sets for domesticated animals and plants, these studies provide novel insights into human evolution and the evolutionary consequences of human behaviour that go well beyond those that can be obtained from modern genomic data or the fossil and archaeological records alone.
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Affiliation(s)
- Stephanie Marciniak
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - George H Perry
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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13
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Dogs' recognition of human selfish and generous attitudes requires little but critical experience with people. PLoS One 2017; 12:e0185696. [PMID: 29045426 PMCID: PMC5646781 DOI: 10.1371/journal.pone.0185696] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 09/18/2017] [Indexed: 12/04/2022] Open
Abstract
There is some dispute regarding the role of experience in the development of dogs´ socio-cognitive abilities in their interaction with people. We sought to provide new evidence to this debate by comparing dogs with contrasting levels of experience with humans, in a task involving the discrimination of human generous and selfish attitudes. To this end, we compared the performance of adult family dogs against that of adult shelter dogs and puppies living in people´s homes. In training trials, the generous experimenter (G) signaled the bowl with food and allowed the dog to eat, whereas the selfish experimenter (S) also signaled the baited bowl, but she/he ate the food before the dog could have access to it. Then, subjects were allowed to freely choose between G and S in the choice test. The main finding was that adult subjects (both family and shelter dogs) developed a preference for G over S, but puppies did not. We conclude that the quality and/or quantity of everyday-contact with people did not affect the discrimination of human attitudes in the present protocol, but the amount of experience with people (in years) did matter. Finally, we discuss the relative role of domestication and ontogeny in the development of dogs´ socio-cognitive abilities.
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14
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Three-Dimensional Geometric Morphometric Analysis of Fossil Canid Mandibles and Skulls. Sci Rep 2017; 7:9508. [PMID: 28842717 PMCID: PMC5573390 DOI: 10.1038/s41598-017-10232-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 08/08/2017] [Indexed: 01/25/2023] Open
Abstract
Much of the fossil record for dogs consists of mandibles. However, can fossil canid mandibles be reliably identified as dogs or wolves? 3D geometric morphometric analysis correctly classifies 99.5% of the modern dog and wolf mandibles. However, only 4 of 26 Ust’-Polui fossil mandibles, a Russian Arctic site occupied from 250BCE to 150CE, were identified as dogs and none of the 20 Ivolgin mandibles, an Iron Age site in southern Russia, were identified as dogs. Three of the Ust’-Polui mandibles and 8 of the Ivolgin mandibles were identified as wolves. In contrast, all 12 Ivolgin skulls and 5 Ust’-Polui skulls were clearly identified as dogs. Only the classification of the UP6571 skull as a dog (Dog Posterior Probability = 1.0) was not supported by the typical probability. Other evidence indicates these canids were domesticated: they were located within human dwellings, remains at both sites have butchery marks indicating that they were consumed, and isotope analysis of canid and human remains from Ust’-Polui demonstrate that both were consuming freshwater protein; indicating that the humans were feeding the canids. Our results demonstrate that the mandible may not evolve as rapidly as the cranium and the mandible is not reliable for identifying early dog fossils.
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15
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Sullivan AP, Bird DW, Perry GH. Human behaviour as a long-term ecological driver of non-human evolution. Nat Ecol Evol 2017; 1:65. [DOI: 10.1038/s41559-016-0065] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 12/20/2016] [Indexed: 12/26/2022]
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16
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The interrelated effect of sleep and learning in dogs (Canis familiaris); an EEG and behavioural study. Sci Rep 2017; 7:41873. [PMID: 28165489 PMCID: PMC5292958 DOI: 10.1038/srep41873] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 12/30/2016] [Indexed: 01/18/2023] Open
Abstract
The active role of sleep in memory consolidation is still debated, and due to a large between-species variation, the investigation of a wide range of different animal species (besides humans and laboratory rodents) is necessary. The present study applied a fully non-invasive methodology to study sleep and memory in domestic dogs, a species proven to be a good model of human awake behaviours. Polysomnography recordings performed following a command learning task provide evidence that learning has an effect on dogs’ sleep EEG spectrum. Furthermore, spectral features of the EEG were related to post-sleep performance improvement. Testing an additional group of dogs in the command learning task revealed that sleep or awake activity during the retention interval has both short- and long-term effects. This is the first evidence to show that dogs’ human-analogue social learning skills might be related to sleep-dependent memory consolidation.
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17
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Druzhkova AS, Makunin AI, Vorobieva NV, Vasiliev SK, Ovodov ND, Shunkov MV, Trifonov VA, Graphodatsky AS. Complete mitochondrial genome of an extinct Equus (Sussemionus) ovodovi specimen from Denisova cave (Altai, Russia). MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:79-81. [PMID: 33473722 PMCID: PMC7800821 DOI: 10.1080/23802359.2017.1285209] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Sussemionus is an extinct subgenus of Equus first characterized and delineated in 2010. The almost complete mitochondrial genome is available only for a single specimen of Sussemionus – a 40,000 years old E. ovodovi from Proskuryakova cave (Khakassia, Russia). Our studies of ancient horses from Denisova cave (Altai, Russia) revealed mitochondrial DNA of this species in a 32,000 years old sample. Using alignments to multiple mitochondrial genomes of non-caballine equids, we recovered 100% complete mitochondrial genome of E. ovodovi for the first time. Phylogenetic analysis demonstrates close relationship between this individual and the one previously described in Khakassia.
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Affiliation(s)
- Anna S Druzhkova
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Alexey I Makunin
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Nadezhda V Vorobieva
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Sergey K Vasiliev
- Institute of Archaeology and Ethnography SB RAS, Novosibirsk, Russia
| | - Nikolai D Ovodov
- Institute of Archaeology and Ethnography SB RAS, Novosibirsk, Russia
| | - Mikhail V Shunkov
- Institute of Archaeology and Ethnography SB RAS, Novosibirsk, Russia
| | - Vladimir A Trifonov
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Alexander S Graphodatsky
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
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18
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Dyomin AG, Danilova MI, Mwacharo JM, Masharsky AE, Panteleev AV, Druzhkova AS, Trifonov VA, Galkina SA. Mitochondrial DNA D-loop haplogroup contributions to the genetic diversity of East European domestic chickens from Russia. J Anim Breed Genet 2016; 134:98-108. [PMID: 27988972 DOI: 10.1111/jbg.12248] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 11/07/2016] [Indexed: 12/22/2022]
Abstract
To elucidate geographical and historical aspects of chicken dispersal across Eastern Europe, we analysed the complete mitochondrial DNA D-loop sequence of 86 representatives from chicken breeds traditionally raised in the territory of the East European Plain (Orloff, Pavlov, Russian White, Yurlov Crower, Uzbek Game and Naked Neck). From the 1231-1232 bp D-loop sequence, 35 variable sites that defined 22 haplotypes were identified in modern chicken. All populations, except Uzbek Game, exhibited high values of haplotype and nucleotide diversity suggesting a wide variation in maternal diversity. Inclusion of mtDNA sequences from other European and Asian countries revealed representatives from this study belonging to haplogroups A, E1 and C1. We also assessed fossil chicken material dated to the 9th-18th century from archaeological sites in Northern and Eastern Europe. Three haplotypes found in the fossil specimens belonged to haplogroup E1, while one sample dated to the 18th century was assigned to the C1 haplogroup. This is the first report of the occurrence of the C1 haplogroup in European chicken populations prior to the 20th century based on the fossil material. These results provide evidence for a relatively recent introduction of all haplotypes other than E1 into the East European chicken gene pool with the significant impact of the C1 haplogroup mainly distributed in Southern China.
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Affiliation(s)
- A G Dyomin
- Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - M I Danilova
- Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - J M Mwacharo
- Centre for Genetics and Genomics, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - A E Masharsky
- Research Resource Centre for Molecular and Cell Technologies, Saint Petersburg State University, Saint Petersburg, Russia
| | - A V Panteleev
- The Ornithology Department, Zoological Institute, Russian Academy of Science, Saint Petersburg, Russia
| | - A S Druzhkova
- Department of Genomic Diversity and Evolution, Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - V A Trifonov
- Department of Genomic Diversity and Evolution, Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - S A Galkina
- Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
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19
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Abstract
Understanding the timing and geographic context of dog origins is a crucial component for understanding human history, as well as the evolutionary context in which the morphological and behavioral divergence of dogs from wolves occurred. A substantial challenge to understanding domestication is that dogs have experienced a complicated demographic history. An initial severe bottleneck was associated with domestication followed by postdivergence gene flow between dogs and wolves, as well as population expansions, contractions, and replacements. In addition, because the domestication of dogs occurred in the relatively recent past, much of the observed polymorphism may be shared between dogs and wolves, limiting the power to distinguish between alternative models of dog history. Greater insight into the domestication process will require explicit tests of alternative models of domestication through the joint analysis of whole genomes from modern lineages and ancient wolves and dogs from across Eurasia.
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Affiliation(s)
- Adam H Freedman
- Informatics Group, Faculty of Arts & Sciences, Harvard University, Cambridge, Massachusetts 02138
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095;
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20
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Ollivier M, Tresset A, Bastian F, Lagoutte L, Axelsson E, Arendt ML, Bălăşescu A, Marshour M, Sablin MV, Salanova L, Vigne JD, Hitte C, Hänni C. Amy2B copy number variation reveals starch diet adaptations in ancient European dogs. ROYAL SOCIETY OPEN SCIENCE 2016; 3:160449. [PMID: 28018628 PMCID: PMC5180126 DOI: 10.1098/rsos.160449] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 10/13/2016] [Indexed: 05/26/2023]
Abstract
Extant dog and wolf DNA indicates that dog domestication was accompanied by the selection of a series of duplications on the Amy2B gene coding for pancreatic amylase. In this study, we used a palaeogenetic approach to investigate the timing and expansion of the Amy2B gene in the ancient dog populations of Western and Eastern Europe and Southwest Asia. Quantitative polymerase chain reaction was used to estimate the copy numbers of this gene for 13 ancient dog samples, dated to between 15 000 and 4000 years before present (cal. BP). This evidenced an increase of Amy2B copies in ancient dogs from as early as the 7th millennium cal. BP in Southeastern Europe. We found that the gene expansion was not fixed across all dogs within this early farming context, with ancient dogs bearing between 2 and 20 diploid copies of the gene. The results also suggested that selection for the increased Amy2B copy number started 7000 years cal. BP, at the latest. This expansion reflects a local adaptation that allowed dogs to thrive on a starch rich diet, especially within early farming societies, and suggests a biocultural coevolution of dog genes and human culture.
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Affiliation(s)
- Morgane Ollivier
- CNRS/ENS de Lyon, French National Platform of Paleogenetics, PALGENE, Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France
- Laboratoire d'Ecologie Alpine (LECA), Université Grenoble Alpes, 38000 Grenoble, France
| | - Anne Tresset
- CNRS/MNHN/SUs-UMR 7209 Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements, 55 rue Buffon, 75005 Paris, France
| | - Fabiola Bastian
- CNRS/ENS de Lyon, French National Platform of Paleogenetics, PALGENE, Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France
- Laboratoire d'Ecologie Alpine (LECA), Université Grenoble Alpes, 38000 Grenoble, France
| | - Laetitia Lagoutte
- Institut de Génétique et Développement de Rennes, CNRS-UMR6290, Université de Rennes1, 35000 Rennes, France
| | - Erik Axelsson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75237 Uppsala, Sweden
| | - Maja-Louise Arendt
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75237 Uppsala, Sweden
| | - Adrian Bălăşescu
- The National Museum of Romanian History, 12 Calea Victoriei, 030026 Bucharest, Romania
| | - Marjan Marshour
- CNRS/MNHN/SUs-UMR 7209 Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements, 55 rue Buffon, 75005 Paris, France
| | - Mikhail V. Sablin
- Russian Academy of Science, Zoological Institute, Saint Petersburg, Russia
| | | | - Jean-Denis Vigne
- CNRS/MNHN/SUs-UMR 7209 Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements, 55 rue Buffon, 75005 Paris, France
| | - Christophe Hitte
- Institut de Génétique et Développement de Rennes, CNRS-UMR6290, Université de Rennes1, 35000 Rennes, France
| | - Catherine Hänni
- CNRS/ENS de Lyon, French National Platform of Paleogenetics, PALGENE, Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France
- Laboratoire d'Ecologie Alpine (LECA), Université Grenoble Alpes, 38000 Grenoble, France
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21
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Janssens LAA, Street M, Miller R, Hazewinkel HAW, Giemsch L, Schmitz R. The oldest case yet reported of osteoarthritis in a dog: an archaeological and radiological evaluation. J Small Anim Pract 2016; 57:568-574. [PMID: 27581723 DOI: 10.1111/jsap.12548] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 04/22/2016] [Accepted: 05/06/2016] [Indexed: 11/28/2022]
Abstract
A century ago the remains of a dog skeleton were found in an archaeological double human burial, near Bonn-Oberkassel (Germany). Recent re-examination of the dog remains revealed that they were about 14,500 years old. Based on the growth plates, the animal was considered to be approximately 7·5 months old at the time of death. Based on the minimal humeral diameter, it was calculated that it was approximately 0·47 m tall at the shoulder and weighed approximately 15·7 kg. The right proximal ulna of this skeleton showed osteoarthritis, manifested by an osteophyte of 5×3×1·5 mm3 at its cranial edge, with no identified primary developmental causes for osteoarthritis. Osteochondritis dissecans, joint incongruity and trauma are possible aetiologies. The left ulna did not reveal any abnormalities.
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Affiliation(s)
- L A A Janssens
- Clinic for Orthopaedic Surgery of Companion Animals, 3068SB Rotterdam, The Netherlands. .,Department of Archaeology, University of Leiden, 2333 CC Leiden, The Netherlands.
| | - M Street
- Monrepos Archaeological Research Centre and Museum for Human Behavioural Evolution, 56567 Neuwied, Germany
| | - R Miller
- Service of Prehistory, University of Liège, 4000 Liège, Belgium
| | - H A W Hazewinkel
- Department of Clinical Sciences of Companion Animals, Utrecht University, 3508TD Utrecht, The Netherlands
| | - L Giemsch
- Archäologisches Museum Frankfurt, Karmelitergasse 1D-60311 Frankfurt am Main, Germany
| | - R Schmitz
- LVR-Landesmuseum Bonn, Rheinisches Landesmuseum für Archäologie, Kunst- und Kulturgeschichte, Bachstraße 5-953115 Bonn, Germany
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22
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Ohkita M, Nagasawa M, Kazutaka M, Kikusui T. Owners' direct gazes increase dogs' attention-getting behaviors. Behav Processes 2016; 125:96-100. [PMID: 26915425 DOI: 10.1016/j.beproc.2016.02.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 01/24/2016] [Accepted: 02/19/2016] [Indexed: 10/22/2022]
Abstract
This study examined whether dogs gain information about human's attention via their gazes and whether they change their attention-getting behaviors (i.e., whining and whimpering, looking at their owners' faces, pawing, and approaching their owners) in response to their owners' direct gazes. The results showed that when the owners gazed at their dogs, the durations of whining and whimpering and looking at the owners' faces were longer than when the owners averted their gazes. In contrast, there were no differences in duration of pawing and likelihood of approaching the owners between the direct and averted gaze conditions. Therefore, owners' direct gazes increased the behaviors that acted as distant signals and did not necessarily involve touching the owners. We suggest that dogs are sensitive to human gazes, and this sensitivity may act as attachment signals to humans, and may contribute to close relationships between humans and dogs.
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Affiliation(s)
| | - Miho Nagasawa
- Jichi Medical University, Japan; Azabu University, Japan
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23
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Janssens L, Spanoghe I, Miller R, Van Dongen S. Can orbital angle morphology distinguish dogs from wolves? ZOOMORPHOLOGY 2015; 135:149-158. [PMID: 26893534 PMCID: PMC4742516 DOI: 10.1007/s00435-015-0294-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Revised: 12/06/2015] [Accepted: 12/08/2015] [Indexed: 02/03/2023]
Abstract
For more than a century, the orbital angle has been studied by many authors to distinguish dog skulls from their progenitor, the wolf. In early studies, the angle was reported to be different between dogs (49°-55°) and wolves (39°-46°). This clear difference was, however, questioned in a more recent Scandinavian study that shows some overlap. It is clear that in all studies several methodological issues were unexplored or unclear and that group sizes and the variety of breeds and wolf subspecies were small. Archaeological dog skulls had also not been studied. Our goal was to test larger and more varied groups and add archaeological samples as they are an evolutionary stage between wolves and modern dogs. We also tested the influence of measuring methods, intra- and inter-reliability, angle symmetry, the influence of variations in skull position and the possibility of measuring and comparing this angle on 3D CT scan images. Our results indicate that there is about 50 % overlap between the angle range in wolves and modern dogs. However, skulls with a very narrow orbital angle were only found in wolves and those with a very wide angle only in dogs. Archaeological dogs have a mean angle very close to the one of the wolves. Symmetry is highest in wolves and lowest in archaeological dogs. The measuring method is very reliable, for both inter- and intra-reliability (0.99-0.97), and most skull position changes have no statistical influence on the angle measured. Three-dimensional CT scan images can be used to measure OA, but the angles differ from direct measuring and cannot be used for comparison. Evolutionary changes in dog skulls responsible for the wider OA compared to wolf skulls are mainly the lateralisation of the zygomatic process of the frontal bone. Our conclusion is that the orbital angle can be used as an additional morphological measuring method to discern wolves from recent and archaeological dogs. Angles above 60° are certainly from recent dogs. Angles under 35° are certainly of wolves.
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Affiliation(s)
- Luc Janssens
- Department of Archaeology, Leiden University, Einsteinweg 2, 2333 CC Leiden, The Netherlands
| | | | - Rebecca Miller
- Service of Prehistory, University of Liège, Quai Roosevelt, 1, 4000 Liège, Belgium
| | - Stefan Van Dongen
- Department of Evolutionary Ecology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
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24
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Galvan M, Vonk J. Man's other best friend: domestic cats (F. silvestris catus) and their discrimination of human emotion cues. Anim Cogn 2015; 19:193-205. [PMID: 26400749 DOI: 10.1007/s10071-015-0927-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 08/20/2015] [Accepted: 09/15/2015] [Indexed: 11/29/2022]
Abstract
The ability of domestic dogs (C. lupus famaliaris) to follow and attend to human emotion expressions is well documented. It is unknown whether domestic cats (F. silvestris catus) possess similar abilities. Because cats belong to the same order (Carnivora), but did not evolve to live in complex social groups, research with them enables us to tease apart the influence of social structure versus domestication processes on the capacity to recognize human communicative cues, such as emotions. Two experiments were conducted to determine the extent to which domestic cats discriminate between human emotion cues. The first experiment presented cats with facial and postural cues of happiness and anger from both an unfamiliar experimenter and their familiar owner in the absence of vocal cues. The second experiment presented cats with vocal cues of human emotion through a positively or negatively charged conversation between an experimenter and owner. Domestic cats were only modestly sensitive to emotion, particularly when displayed by their owner, suggesting that a history of human interaction alone may not be sufficient to shape such abilities in domestic cats.
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Affiliation(s)
- Moriah Galvan
- Department of Psychology, Oakland University, 2200 N Squirrel Rd., Rochester, MI, 48309, USA
| | - Jennifer Vonk
- Department of Psychology, Oakland University, 2200 N Squirrel Rd., Rochester, MI, 48309, USA.
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25
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Parker HG, Gilbert SF. From caveman companion to medical innovator: genomic insights into the origin and evolution of domestic dogs. ACTA ACUST UNITED AC 2015; 5:239-255. [PMID: 28490917 DOI: 10.2147/agg.s57678] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The phenotypic and behavioral diversity of the domestic dog has yet to be matched by any other mammalian species. In their current form, which comprises more than 350 populations known as breeds, there is a size range of two orders of magnitude and morphological features reminiscent of not only different species but also different phylogenetic families. The range of both appearance and behavior found in the dog is the product of millennia of human interference, and though humans created the diversity it remains a point of fascination to both lay and scientific communities. In this review we summarize the current understanding of the history of dog domestication based on molecular data. We will examine the ways that canine genetic and genomic studies have evolved and look at examples of dog genetics in the light of human disease.
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Affiliation(s)
- Heidi G Parker
- National Human Genome Research Institute, National Institutes of Health, Bethesda MD, 20892 USA
| | - Samuel F Gilbert
- National Human Genome Research Institute, National Institutes of Health, Bethesda MD, 20892 USA
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26
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Druzhkova AS, Vorobieva NV, Trifonov VA, Graphodatsky AS. Ancient DNA: Results and prospects (The 30th anniversary). RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415060046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Lee EJ, Merriwether DA, Kasparov AK, Nikolskiy PA, Sotnikova MV, Pavlova EY, Pitulko VV. Ancient DNA analysis of the oldest canid species from the Siberian Arctic and genetic contribution to the domestic dog. PLoS One 2015; 10:e0125759. [PMID: 26018528 PMCID: PMC4446326 DOI: 10.1371/journal.pone.0125759] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 03/26/2015] [Indexed: 11/18/2022] Open
Abstract
Modern Arctic Siberia provides a wealth of resources for archaeological, geological, and paleontological research to investigate the population dynamics of faunal communities from the Pleistocene, particularly as the faunal material coming from permafrost has proven suitable for genetic studies. In order to examine the history of the Canid species in the Siberian Arctic, we carried out genetic analysis of fourteen canid remains from various sites, including the well-documented Upper Paleolithic Yana RHS and Early Holocene Zhokhov Island sites. Estimated age of samples range from as recent as 1,700 years before present (YBP) to at least 360,000 YBP for the remains of the extinct wolf, Canis cf. variabilis. In order to examine the genetic affinities of ancient Siberian canids species to the domestic dog and modern wolves, we obtained mitochondrial DNA control region sequences and compared them to published ancient and modern canid sequences. The older canid specimens illustrate affinities with pre-domestic dog/wolf lineages while others appear in the major phylogenetic clades of domestic dogs. Our results suggest a European origin of domestic dog may not be conclusive and illustrates an emerging complexity of genetic contribution of regional wolf breeds to the modern Canis gene pool.
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Affiliation(s)
- Esther J. Lee
- Department of Anthropology, Binghamton University, Binghamton, NY, United States of America
- Department of Sociology, Anthropology, and Social Work, Texas Tech University, Lubbock, TX, United States of America
- * E-mail:
| | - D. Andrew Merriwether
- Department of Anthropology, Binghamton University, Binghamton, NY, United States of America
| | - Alexei K. Kasparov
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
| | | | | | | | - Vladimir V. Pitulko
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
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Skoglund P, Ersmark E, Palkopoulou E, Dalén L. Ancient wolf genome reveals an early divergence of domestic dog ancestors and admixture into high-latitude breeds. Curr Biol 2015; 25:1515-9. [PMID: 26004765 DOI: 10.1016/j.cub.2015.04.019] [Citation(s) in RCA: 231] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 03/11/2015] [Accepted: 04/10/2015] [Indexed: 11/17/2022]
Abstract
The origin of domestic dogs is poorly understood [1-15], with suggested evidence of dog-like features in fossils that predate the Last Glacial Maximum [6, 9, 10, 14, 16] conflicting with genetic estimates of a more recent divergence between dogs and worldwide wolf populations [13, 15, 17-19]. Here, we present a draft genome sequence from a 35,000-year-old wolf from the Taimyr Peninsula in northern Siberia. We find that this individual belonged to a population that diverged from the common ancestor of present-day wolves and dogs very close in time to the appearance of the domestic dog lineage. We use the directly dated ancient wolf genome to recalibrate the molecular timescale of wolves and dogs and find that the mutation rate is substantially slower than assumed by most previous studies, suggesting that the ancestors of dogs were separated from present-day wolves before the Last Glacial Maximum. We also find evidence of introgression from the archaic Taimyr wolf lineage into present-day dog breeds from northeast Siberia and Greenland, contributing between 1.4% and 27.3% of their ancestry. This demonstrates that the ancestry of present-day dogs is derived from multiple regional wolf populations.
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Affiliation(s)
- Pontus Skoglund
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden.
| | - Erik Ersmark
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
| | - Eleftheria Palkopoulou
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden.
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Carballo F, Freidin E, Bentosela M. Estudios Sobre Cooperación en Perros Domésticos: una Revisión Crítica. REVISTA COLOMBIANA DE PSICOLOGÍA 2015. [DOI: 10.15446/rcp.v24n1.41221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
El análisis comparado de la cooperación contribuye al entendimiento tanto de sus orígenes evolutivos como de los mecanismos próximos involucrados en dicho fenómeno. Esta revisión se centra en estudios sobre cooperación en perros domésticos. Para ello se definieron conceptos relacionados con la cooperación, se describieron las razones filogenéticas y ontogenéticas que hacen del perro un buen modelo para el estudio de este fenómeno y se hizo una revisión crítica de los trabajos realizados en este campo. Fueron incluidas investigaciones sobre situaciones cooperativas y sobre las habilidades cognitivas involucradas. Se discuten hipótesis sobre los mecanismos próximos de esta habilidad que incluyen elementos emocionales, motivacionales y de aprendizaje asociativo.
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Fregel R, Suárez NM, Betancor E, González AM, Cabrera VM, Pestano J. Mitochondrial DNA haplogroup phylogeny of the dog: Proposal for a cladistic nomenclature. Mitochondrion 2015; 22:75-84. [PMID: 25869968 DOI: 10.1016/j.mito.2015.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 09/27/2014] [Accepted: 04/02/2015] [Indexed: 10/23/2022]
Abstract
Canis lupus familiaris mitochondrial DNA analysis has increased in recent years, not only for the purpose of deciphering dog domestication but also for forensic genetic studies or breed characterization. The resultant accumulation of data has increased the need for a normalized and phylogenetic-based nomenclature like those provided for human maternal lineages. Although a standardized classification has been proposed, haplotype names within clades have been assigned gradually without considering the evolutionary history of dog mtDNA. Moreover, this classification is based only on the D-loop region, proven to be insufficient for phylogenetic purposes due to its high number of recurrent mutations and the lack of relevant information present in the coding region. In this study, we design 1) a refined mtDNA cladistic nomenclature from a phylogenetic tree based on complete sequences, classifying dog maternal lineages into haplogroups defined by specific diagnostic mutations, and 2) a coding region SNP analysis that allows a more accurate classification into haplogroups when combined with D-loop sequencing, thus improving the phylogenetic information obtained in dog mitochondrial DNA studies.
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Affiliation(s)
- Rosa Fregel
- Department of Genetics, Faculty of Medicine, University of Las Palmas de Gran Canaria, Las Palmas, Spain; Department of Genetics, Faculty of Biology, University of La Laguna, La Laguna, Spain.
| | - Nicolás M Suárez
- Department of Genetics, Faculty of Medicine, University of Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Eva Betancor
- Forensic Genetics Laboratory, Institute of Legal Medicine of Las Palmas, Las Palmas, Spain
| | - Ana M González
- Department of Genetics, Faculty of Biology, University of La Laguna, La Laguna, Spain
| | - Vicente M Cabrera
- Department of Genetics, Faculty of Biology, University of La Laguna, La Laguna, Spain
| | - José Pestano
- Department of Genetics, Faculty of Medicine, University of Las Palmas de Gran Canaria, Las Palmas, Spain; Forensic Genetics Laboratory, Institute of Legal Medicine of Las Palmas, Las Palmas, Spain
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Carballo F, Freidin E, Putrino N, Shimabukuro C, Casanave E, Bentosela M. Dog's discrimination of human selfish and generous attitudes: the role of individual recognition, experience, and experimenters' gender. PLoS One 2015; 10:e0116314. [PMID: 25714915 PMCID: PMC4340621 DOI: 10.1371/journal.pone.0116314] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 12/09/2014] [Indexed: 11/18/2022] Open
Abstract
Discrimination of and memory for others' generous and selfish behaviors could be adaptive abilities in social animals. Dogs have seemingly expressed such skills in both direct and indirect interactions with humans. However, recent studies suggest that their capacity may rely on cues other than people's individual characteristics, such as the place where the person stands. Thus, the conditions under which dogs recognize individual humans when solving cooperative tasks still remains unclear. With the aim of contributing to this problem, we made dogs interact with two human experimenters, one generous (pointed towards the food, gave ostensive cues, and allowed the dog to eat it) and the other selfish (pointed towards the food, but ate it before the dog could have it). Then subjects could choose between them (studies 1-3). In study 1, dogs took several training trials to learn the discrimination between the generous and the selfish experimenters when both were of the same gender. In study 2, the discrimination was learned faster when the experimenters were of different gender as evidenced both by dogs' latencies to approach the bowl in training trials as well as by their choices in preference tests. Nevertheless, dogs did not get confused by gender when the experimenters were changed in between the training and the choice phase in study 3. We conclude that dogs spontaneously used human gender as a cue to discriminate between more and less cooperative experimenters. They also relied on some other personal feature which let them avoid being confused by gender when demonstrators were changed. We discuss these results in terms of dogs' ability to recognize individuals and the potential advantage of this skill for their lives in human environments.
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Affiliation(s)
- Fabricio Carballo
- Canid Behavior Research Group (ICOC), Medical Research Institute (IDIM; CONICET-UBA), Buenos Aires, Argentina
- Instituto de Investigaciones Biológicas y Biomédicas del Sur (INBIOSUR; CONICET-UNS), Bahía Blanca, Argentina
| | - Esteban Freidin
- Canid Behavior Research Group (ICOC), Medical Research Institute (IDIM; CONICET-UBA), Buenos Aires, Argentina
- Instituto de Investigaciones Económicas y Sociales del Sur (IIESS; CONICET-UNS), Bahía Blanca, Argentina
| | - Natalia Putrino
- Canid Behavior Research Group (ICOC), Medical Research Institute (IDIM; CONICET-UBA), Buenos Aires, Argentina
| | - Carolina Shimabukuro
- Canid Behavior Research Group (ICOC), Medical Research Institute (IDIM; CONICET-UBA), Buenos Aires, Argentina
| | - Emma Casanave
- Instituto de Investigaciones Biológicas y Biomédicas del Sur (INBIOSUR; CONICET-UNS), Bahía Blanca, Argentina
| | - Mariana Bentosela
- Canid Behavior Research Group (ICOC), Medical Research Institute (IDIM; CONICET-UBA), Buenos Aires, Argentina
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Witt KE, Judd K, Kitchen A, Grier C, Kohler TA, Ortman SG, Kemp BM, Malhi RS. DNA analysis of ancient dogs of the Americas: identifying possible founding haplotypes and reconstructing population histories. J Hum Evol 2014; 79:105-18. [PMID: 25532803 DOI: 10.1016/j.jhevol.2014.10.012] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 06/16/2014] [Accepted: 10/22/2014] [Indexed: 11/13/2022]
Abstract
As dogs have traveled with humans to every continent, they can potentially serve as an excellent proxy when studying human migration history. Past genetic studies into the origins of Native American dogs have used portions of the hypervariable region (HVR) of mitochondrial DNA (mtDNA) to indicate that prior to European contact the dogs of Native Americans originated in Eurasia. In this study, we summarize past DNA studies of both humans and dogs to discuss their population histories in the Americas. We then sequenced a portion of the mtDNA HVR of 42 pre-Columbian dogs from three sites located in Illinois, coastal British Columbia, and Colorado, and identify four novel dog mtDNA haplotypes. Next, we analyzed a dataset comprised of all available ancient dog sequences from the Americas to infer the pre-Columbian population history of dogs in the Americas. Interestingly, we found low levels of genetic diversity for some populations consistent with the possibility of deliberate breeding practices. Furthermore, we identified multiple putative founding haplotypes in addition to dog haplotypes that closely resemble those of wolves, suggesting admixture with North American wolves or perhaps a second domestication of canids in the Americas. Notably, initial effective population size estimates suggest at least 1000 female dogs likely existed in the Americas at the time of the first known canid burial, and that population size increased gradually over time before stabilizing roughly 1200 years before present.
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Affiliation(s)
- Kelsey E Witt
- School of Integrative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Kathleen Judd
- Kemp Lab of Molecular Anthropology and Ancient DNA, Washington State University, Pullman, WA 99164, USA
| | - Andrew Kitchen
- Department of Anthropology, University of Iowa, Iowa City, IA 52242, USA
| | - Colin Grier
- Department of Anthropology, Washington State University, Pullman, WA 99164, USA
| | - Timothy A Kohler
- Department of Anthropology, Washington State University, Pullman, WA 99164, USA; Santa Fe Institute, Santa Fe, NM 87501, USA; Crow Canyon Archaeological Center, 23390 Road K, Cortez, CO 81321-9408, USA
| | - Scott G Ortman
- Department of Anthropology, University of Colorado, Boulder, CO 80309, USA
| | - Brian M Kemp
- Department of Anthropology, Washington State University, Pullman, WA 99164, USA; School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Ripan S Malhi
- School of Integrative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Department of Anthropology and Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61802, USA.
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Genome-wide identification and analysis of basic helix-loop-helix domains in dog, Canis lupus familiaris. Mol Genet Genomics 2014; 290:633-48. [PMID: 25403511 DOI: 10.1007/s00438-014-0950-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 10/30/2014] [Indexed: 01/04/2023]
Abstract
The basic helix-loop-helix (bHLH) domain is a highly conserved amino acid motif that defines a group of DNA-binding transcription factors. bHLH proteins play essential regulatory roles in a variety of biological processes in animal, plant, and fungus. The domestic dog, Canis lupus familiaris, is a good model organism for genetic, physiological, and behavioral studies. In this study, we identified 115 putative bHLH genes in the dog genome. Based on a phylogenetic analysis, 51, 26, 14, 4, 12, and 4 dog bHLH genes were assigned to six separate groups (A-F); four bHLH genes were categorized as ''orphans''. Within-group evolutionary relationships inferred from the phylogenetic analysis were consistent with positional conservation, other conserved domains flanking the bHLH motif, and highly conserved intron/exon patterns in other vertebrates. Our analytical results confirmed the GenBank annotations of 89 dog bHLH proteins and provided information that could be used to update the annotations of the remaining 26 dog bHLH proteins. These data will provide good references for further studies on the structures and regulatory functions of bHLH proteins in the growth and development of dogs, which may help in understanding the mechanisms that underlie the physical and behavioral differences between dogs and wolves.
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Lingle S, Riede T. Deer Mothers Are Sensitive to Infant Distress Vocalizations of Diverse Mammalian Species. Am Nat 2014; 184:510-22. [DOI: 10.1086/677677] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Blasco R, Finlayson C, Rosell J, Marco AS, Finlayson S, Finlayson G, Negro JJ, Pacheco FG, Vidal JR. The earliest pigeon fanciers. Sci Rep 2014; 4:5971. [PMID: 25101932 PMCID: PMC4124739 DOI: 10.1038/srep05971] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 07/18/2014] [Indexed: 11/26/2022] Open
Abstract
Feral Pigeons have colonised all corners of the Earth, having developed a close association with humans and their activities. The wild ancestor of the Feral Pigeon, the Rock Dove, is a species of rocky habitats, nesting typically on cliff ledges and at the entrance to large caves. This habit would have brought them into close contact with cave-dwelling humans, a relationship usually linked to the development of dwellings in the Neolithic. We show that the association between humans and Rock Doves is an ancient one with its roots in the Palaeolithic and predates the arrival of modern humans into Europe. At Gorham's Cave, Gibraltar, the Neanderthals exploited Rock Doves for food for a period of over 40 thousand years, the earliest evidence dating to at least 67 thousand years ago. We show that the exploitation was not casual or sporadic, having found repeated evidence of the practice in different, widely spaced, temporal contexts within the cave. Our results point to hitherto unappreciated capacities of the Neanderthals to exploit birds as food resources on a regular basis. More so, they were practising it long before the arrival of modern humans and had therefore invented it independently.
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Affiliation(s)
- Ruth Blasco
- The Gibraltar Museum, 18-20 Bomb House Lane, P. O. Box 939, Gibraltar
| | - Clive Finlayson
- The Gibraltar Museum, 18-20 Bomb House Lane, P. O. Box 939, Gibraltar
| | - Jordi Rosell
- 1] Àrea de Prehistòria, Universitat Rovira i Virgili (URV), Avinguda de Catalunya 35, 43002 Tarragona, Spain [2] IPHES, Institut Català de Paleoecologia Humana i Evolució Social, C/Marcel.lí Domingo s/n - Campus Sescelades URV (Edifici W3), 43007 Tarragona, Spain
| | - Antonio Sánchez Marco
- Area of Neogene and Quaternary Faunas, Institut Català de Paleontologia, Campus de la UAB, Cerdanyola del Vallès, Barcelona, Spain
| | - Stewart Finlayson
- The Gibraltar Museum, 18-20 Bomb House Lane, P. O. Box 939, Gibraltar
| | | | - Juan José Negro
- Estación Biológica de Doñana (CSIC), Department of Evolutionary Ecology, Avda. Americo Vespucio s/n, 41092 Sevilla, Spain
| | | | - Joaquín Rodríguez Vidal
- Depto. Geodinámica y Paleontología, Facultad de Ciencias Experimentales, Campus del Carmen, Universidad de Huelva, Marine International Campus of Excellence - CEIMAR, 21071 Huelva, Spain
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Morphological and genetic evidence for early Holocene cattle management in northeastern China. Nat Commun 2014; 4:2755. [PMID: 24202175 DOI: 10.1038/ncomms3755] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Accepted: 10/14/2013] [Indexed: 11/08/2022] Open
Abstract
The domestication of cattle is generally accepted to have taken place in two independent centres: around 10,500 years ago in the Near East, giving rise to modern taurine cattle, and two millennia later in southern Asia, giving rise to zebu cattle. Here we provide firmly dated morphological and genetic evidence for early Holocene management of taurine cattle in northeastern China. We describe conjoining mandibles from this region that show evidence of oral stereotypy, dated to the early Holocene by two independent ¹⁴C dates. Using Illumina high-throughput sequencing coupled with DNA hybridization capture, we characterize 15,406 bp of the mitogenome with on average 16.7-fold coverage. Phylogenetic analyses reveal a hitherto unknown mitochondrial haplogroup that falls outside the known taurine diversity. Our data suggest that the first attempts to manage cattle in northern China predate the introduction of domestic cattle that gave rise to the current stock by several thousand years.
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Paedomorphic facial expressions give dogs a selective advantage. PLoS One 2013; 8:e82686. [PMID: 24386109 PMCID: PMC3873274 DOI: 10.1371/journal.pone.0082686] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 10/27/2013] [Indexed: 11/19/2022] Open
Abstract
How wolves were first domesticated is unknown. One hypothesis suggests that wolves underwent a process of self-domestication by tolerating human presence and taking advantage of scavenging possibilities. The puppy-like physical and behavioural traits seen in dogs are thought to have evolved later, as a byproduct of selection against aggression. Using speed of selection from rehoming shelters as a proxy for artificial selection, we tested whether paedomorphic features give dogs a selective advantage in their current environment. Dogs who exhibited facial expressions that enhance their neonatal appearance were preferentially selected by humans. Thus, early domestication of wolves may have occurred not only as wolf populations became tamer, but also as they exploited human preferences for paedomorphic characteristics. These findings, therefore, add to our understanding of early dog domestication as a complex co-evolutionary process.
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Stahl PW. Early Dogs and Endemic South American Canids of the Spanish Main. JOURNAL OF ANTHROPOLOGICAL RESEARCH 2013. [DOI: 10.3998/jar.0521004.0069.405] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Thalmann O, Shapiro B, Cui P, Schuenemann VJ, Sawyer SK, Greenfield DL, Germonpre MB, Sablin MV, Lopez-Giraldez F, Domingo-Roura X, Napierala H, Uerpmann HP, Loponte DM, Acosta AA, Giemsch L, Schmitz RW, Worthington B, Buikstra JE, Druzhkova A, Graphodatsky AS, Ovodov ND, Wahlberg N, Freedman AH, Schweizer RM, Koepfli KP, Leonard JA, Meyer M, Krause J, Paabo S, Green RE, Wayne RK. Complete Mitochondrial Genomes of Ancient Canids Suggest a European Origin of Domestic Dogs. Science 2013; 342:871-4. [DOI: 10.1126/science.1243650] [Citation(s) in RCA: 348] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Freidin E, Putrino N, D’Orazio M, Bentosela M. Dogs' Eavesdropping from people's reactions in third party interactions. PLoS One 2013; 8:e79198. [PMID: 24236108 PMCID: PMC3827296 DOI: 10.1371/journal.pone.0079198] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 09/19/2013] [Indexed: 11/20/2022] Open
Abstract
Eavesdropping involves the acquisition of information from third-party interactions, and can serve to indirectly attribute reputation to individuals. There is evidence on eavesdropping in dogs, indicating that they can develop a preference for people based on their cooperativeness towards others. In this study, we tested dogs’ eavesdropping abilities one step further. In a first experiment, dogs could choose between cooperative demonstrators (the donors) who always gave food to an approaching third person (the beggar); here, the only difference between donors was whether they received positive or negative reactions from the beggar (through verbal and gestural means). Results showed that dogs preferentially approached the donor who had received positive reactions from the beggar. By contrast, two different conditions showed that neither the beggar’s body gestures nor the verbal component of the interaction on their own were sufficient to affect the dogs’ preferences. We also ran two further experiments to test for the possibility of dogs’ choices being driven by local enhancement. When the donors switched places before the choice, dogs chose at random. Similarly, in a nonsocial condition in which donors were replaced by platforms, subjects chose at chance levels. We conclude that dogs’ nonrandom choices in the present protocol relied on the simultaneous presence of multiple cues, such as the place where donors stood and several features of the beggar’s behavior (gestural and verbal reactions, and eating behavior). Nonetheless, we did not find conclusive evidence that dogs discriminated the donors by their physical features, which is a prerequisite of reputation attribution.
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Affiliation(s)
- Esteban Freidin
- Centro de Recursos Naturales Renovables de la Zona Semiárida, Centro Científico Tecnológico Consejo Nacional de Investigaciones Científicas y Técnicas, Bahía Blanca, Argentina
| | - Natalia Putrino
- Grupo de Investigación del Comportamiento en Cánidos, Instituto de Investigaciones Médicas Alfredo Lanari, Consejo Nacional de Investigaciones Científicas y Técnicas/Universidad de Buenos Aires, Buenos Aires, Argentina
| | - María D’Orazio
- Grupo de Investigación del Comportamiento en Cánidos, Instituto de Investigaciones Médicas Alfredo Lanari, Consejo Nacional de Investigaciones Científicas y Técnicas/Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mariana Bentosela
- Grupo de Investigación del Comportamiento en Cánidos, Instituto de Investigaciones Médicas Alfredo Lanari, Consejo Nacional de Investigaciones Científicas y Técnicas/Universidad de Buenos Aires, Buenos Aires, Argentina
- * E-mail:
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41
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Losey RJ, Garvie-Lok S, Leonard JA, Katzenberg MA, Germonpré M, Nomokonova T, Sablin MV, Goriunova OI, Berdnikova NE, Savel'ev NA. Burying dogs in ancient Cis-Baikal, Siberia: temporal trends and relationships with human diet and subsistence practices. PLoS One 2013; 8:e63740. [PMID: 23696851 PMCID: PMC3656967 DOI: 10.1371/journal.pone.0063740] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Accepted: 04/05/2013] [Indexed: 11/18/2022] Open
Abstract
The first objective of this study is to examine temporal patterns in ancient dog burials in the Lake Baikal region of Eastern Siberia. The second objective is to determine if the practice of dog burial here can be correlated with patterns in human subsistence practices, in particular a reliance on terrestrial mammals. Direct radiocarbon dating of a suite of the region's dog remains indicates that these animals were given burial only during periods in which human burials were common. Dog burials of any kind were most common during the Early Neolithic (∼7-8000 B.P.), and rare during all other time periods. Further, only foraging groups seem to have buried canids in this region, as pastoralist habitation sites and cemeteries generally lack dog interments, with the exception of sacrificed animals. Stable carbon and nitrogen isotope data indicate that dogs were only buried where and when human diets were relatively rich in aquatic foods, which here most likely included river and lake fish and Baikal seal (Phoca sibirica). Generally, human and dog diets appear to have been similar across the study subregions, and this is important for interpreting their radiocarbon dates, and comparing them to those obtained on the region's human remains, both of which likely carry a freshwater old carbon bias. Slight offsets were observed in the isotope values of dogs and humans in our samples, particularly where both have diets rich in aquatic fauna. This may result from dietary differences between people and their dogs, perhaps due to consuming fish of different sizes, or even different tissues from the same aquatic fauna. This paper also provides a first glimpse of the DNA of ancient canids in Northeast Asia.
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Affiliation(s)
- Robert J Losey
- Department of Anthropology, University of Alberta, Edmonton, Alberta, Canada.
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